alignments of DNA sequences

Question

[midox]

Hello,
I have a long sequences file and another small sequences. I want to do an alignment (multiple or global) of small sequences on long sequences.
Do you suggest me the right software? of course I have two files, I do not know if we can make an alignment by taking two fihciers entered into.
thanks for your answers

Answer 1

[stolarek.ir]

EMBOSS
http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html

[midox]

is it the only one that accepts two files?

Answer 2

[piet]

but the alignment tools do not accept two input file.

Adding more sequences to an already existing multi sequence alignment is often called 'profile aligning'. 'mafft' has three options for this purpose (--add, --addfragments, --addfull). Please read the mafft manual.

[midox]

thankyou for your help.
But mafft can't do this.
it uses sequences already aligned then added other sequences.
In my case, I want to align a séqences a file with all sequences of another file (not aligned).

Answer 3

[bshifaw]

You can try blast 2 to perform the alignment (click here). You'll be able to align sequences from one file with sequences of another.

Answer 4

[midox]

here is my problem:
I have a file A of sequences DNA and a file B of sequence DNA.
I want to do a multiple sequence alignment of each sequence in file A with all sequences of B.
The problem is I have two files and according to my research there are no multiple alignment tools that accepts two files.

can you help me

[Adrian Pelin]

Why not just merge the 2 files together and do your alignment? Why would you want to individually align sequences from A with everything from B? If that is really your goal, then you need to create multiple alignment files all consisting of B sequences and a unique A sequence. a script could do this easily, what do the headers look like?

Answer 5

[harold.smith.tarheel]

If the number of of long sequences in the file is not too large, then you can format it as FASTA (if it isn't already) and use it as the reference to align the file of short sequences with any of the short read aligners.

[midox]

but the alignment tools do not accept two input file.
they only accept one file. As muscle or mafft.